[2014-05-29 04:36:51] Beginning TopHat run (v2.0.8b)
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[2014-05-29 04:36:51] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 04:36:51] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 04:36:51] Checking for Bowtie index files
[2014-05-29 04:36:51] Checking for reference FASTA file
[2014-05-29 04:36:51] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 04:36:53] Preparing reads
	 left reads: min. length=60, max. length=101, 22009012 kept reads (1346 discarded)
[2014-05-29 04:45:55] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 05:22:47] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 05:25:51] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 05:29:19] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 05:32:50] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 05:36:24] Searching for junctions via segment mapping
[2014-05-29 05:43:45] Retrieving sequences for splices
[2014-05-29 05:45:46] Indexing splices
[2014-05-29 05:46:35] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 05:48:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 05:51:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 05:53:33] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 05:56:00] Joining segment hits
[2014-05-29 05:59:37] Reporting output tracks
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[2014-05-29 06:14:19] Run complete: 01:37:28 elapsed